The PLATON checkcif and SQUEEZE Tools

Transcription

1 The PLATON checkcif and SQUEEZE Tools Ton Spek Utrecht University, NL Rigaku/Oxford DiffracIon UsermeeIng Wroclaw, june 20, 2016

2 QUESTION: Is this Structure Correct? The Aug IUCr/checkCIF reports no serious ALERTS R1 = wr2 = S = Rhomin Rhomax 0.47 No Voids No Unusual Contacts Normal? Difference Density Range

3 No, The Structure was Deliberately INVENTED This devious structure was clevery created by Natalie Johnson et al., Newcastle, UK, aiming to beat checkcif. It was presented as an excellent Poster during the 2015 ECM Congress in Rovinj, CroaIa. But: Every crime leaves its traces..

4 Clear traces of the Crime are in the Difference Density Map Expected type of difference map Difference map in the CH2 plane The CH2 Hydrogen atoms at calculated posiions are definitely not in F(obs) Unusual Actual difference map Density

5 How was Structure Natalie created? YLID YLID StarIng Material (Bruker) Chemical issue: Se + No example in the CSD for the 6-membered ring System NATALIE Mogul : Se C outlier

6 CURRENT PLATON/CHECKCIF VALIDATION REPORT FOR NATALIE í ë No H-density No Density on Bonds

7 What is PLATON A collecion of SHELX compaible tools bundled in a single program The Toolset includes: CheckCIF (Structure ValidaIon) SQUEEZE (Handling Disordered Solvents) ADDSYM (Missed Symmetry) TwinRotMat (Twinning DetecIon) Bijvoet (Absolute Structure Hoom(y))

8 PLATON/CHECKCIF Is currently the major validaion engine behind the IUCr driven checkcif validaion project of crystal structures. It Checks and Reports on (with ALERTS) Completeness of the supplied informaion Problems with the experimental data Problems with the interpretaion of the data Problems with the reported structure model Unusual structural features

9 Structure ValidaIon now over 20 Years The introducion of the CIF standard for data archival made automaic structure checking possible. Structure validaion provides authors, referees and readers with a list of possibly interesing issues with a structure report that might need to be addressed. Currently about 500 tests have been implemented in checkcif and that number is sill increasing on the basis of newly detected issues with supplied CIF s. ALERTS are not necessarily errors. They omen point at interesing structural features to be discussed.

10 Some ValidaIon Issues A CIF essenially archives the authors interpretaion of the underlying experimental diffracion data. Archived reflecion data are needed for a meaningful evaluaion of unusual results and for test calculaions. Archival of Fo/Fc data (FCF) already solves part of this issue (side effect of its availability: detecion and prove of cases of a few hundred seriously frauded structures in Acta Cryst. E) Recently: embedding of refinement instrucions (res) and unmerged reflecion data (hkl) in the CIF urged. The embedding of the.res &.hkl into the CIF with SHELXL2014 currently voids the need to supply an FCF. IUCr/checkCIF and hkl deposiion are now also part of the CSD deposiion and archival procedures.

11 FCF-ValidaIon adds: Analysis of the quality of the refinement Analysis of the difference map (peaks) DetecIon of void content (SQUEEZE) DetecIon of missing reflecions DetecIon of outliers DetecIon of missed twinning Check of the absolute structure

12 Benefits of the SHELXL2014 standard embedding of.res,.hkl (&.fab) No need to supply an FCF file along with the CIF as part of a data deposiion. The FCF can be created from the embedded data. When supplied, the FCF should be LIST 4 or LIST 8 type SHELXL2014 CIF + FCF are the recommended files to run the SQUEEZE tool since the original reflecion data are retained in the CIF

13 The SQUEEZE Tool STATISTICS PREPARED BY THE CCDC ON SQUEEZEd or OLEX2-MASKd STRUCTURES in the CSD

14 PLATON/SQUEEZE The current implementaion of the SQUEEZE tool to handle disordered solvents is the third generaion of a method published by us more than 25 years ago. Interfacing with SHELXL2014 refinement solves many earlier issues with SHELX76 & SHELXL97 using.res &.hkl data. [e.g. ModificaIon of the observed data] DocumentaIon of the recommended procedure: A.L.Spek (2015) Acta Cryst. C71, 9-18 htp://

15 The Disordered Solvent Problem The calculated structure factor Fc can be spit into two parts: Fc = Fc(model) + Fc(solvent) Fc(solvent) can be parametrized with an (elaborate) disorder model and refined along with the other model parameters. Fc(solvent) can also be approximated with the SQUEEZE tool and used as a fixed contribuion to the structure factors in the refinement. In simple cases, the first approach is preferred

16 The PLATON/SQUEEZE Tool SQUEEZE, as implemented in PLATON, analyses the content of solvent accessible VOID(s) in a crystal structure. (Q: are the voids empty?). The VOID content will generally involve (heavily) disordered solvent(s) that might be difficult to parameterize meaningfully (e.g. unknown solvents). The solvent contribuion to the calculated structure factors is approximated by Fourier transformaion of the density in the VOID(s) as part of the leastsquares refinement of the model parameters. (.fab) SQUEEZE does not refine the Fc(model)

17 The Proper use of SQUEEZE It is important that the final CIF archives both the details of the SQUEEZE calculaion and the unmerged reflecion data. In that way, the calculaions can be reconstructed and/or alternaive refinement models atempted. SHELXL2014 offers all what is needed for that. SQUEEZE uses the model parameters taken from.cif and merged observed structure factors from the LIST 4 or LIST 8.fcf to calculate solvent F(calc) on.fab. Final SHELXL refinement will be based on the CIF embedded.res,.hkl files along with the.fab file.

18 How to SQUEEZE with SHELXL Refine a non-solvent model with name.ins & name.hkl (Include ACTA record, NO LIST 6). 2. Run PLATON/SQUEEZE, based on name.cif & name.fcf from 1 as platon q name.cif. 3. ConInue SHELXL refinement with the files name_sq.ins, name_sq.hkl & name_sq.fab from 2 as shelxl name_sq 4. Inspect the.lis &.lst files and Validate

19 SQUEEZE Disordered Solvent + Twinning Step 1: SHELXL refinement based a name.ins (that should include ACTA, LIST 8, BASF and HKLF 5 [or TWIN ] records) and a name.hkl file Step 2: Run SQUEEZE with the name.cif and name.fcf files produced in Step 1 (i.e. run: platon q name.cif) Step 3: ConInue SHELXL refinement with the files name_sq.ins, name_sq.hkl and name_sq.fab produced by PLATON in step 2 è name_sq.cif & name_sq.fcf Note: The name_sq.fab file contains the solvent contribuion to the SF and the details of SQUEEZE.

20 SQUEEZE-2016 Example: CoordinaIon Compound Acetonitril Model: R = , wr2 = , rho(max) = 1.34 e/a-3 Space Group P2 1 Z = 4, Z = 2 60:40 Twin Twin axis: (0 0 1) 150 K TWINABS hklf5 data Acetonitril solvate Step 1 (SHELXL2014) è R1 = 0.047, wr2 = Step 2 (SQUEEZE) è 177 electrons found in unit cell Step 3 (SHELXL2014) è R1 = , wr2 = , S = 1.064

21 Effect of on R(F) before and amer SQUEEZE as a funcion of sin(theta)/lambda

22 Requirements There should be no residual unresolved density in the discrete model region of the structure because of its impact on the difference map in the solvent region. The data set should be reasonably complete and with sufficient resoluion [i.e. sin(theta)/ lambda >0.6]. There should be no unresolved charge balance issues that might effect the chemistry involved (e.g. The valency of a metal in the ordered part of the structure)

23 LimitaIons The reported electron count in the solvent region is meaningful only with the supply of a complete and reliable reflecion data set. The SQUEEZE technique can not handle properly cases of coupled disorder effecing both the model and the solvent region. The solvent region is assumed not to contain significant anomalous scaterers (Friedels averaged)

24 Thank you! Please send suggesions and examples (with data) of (annoying) issues to: More info: (including this powerpoint presentaion)